This study addresses the issues of the current industry-academy cooperation (IAC) and its effects in Taiwan. The data were drawn from “colleges and universities in Taiwan in 2010 Industry-Academy Cooperation performance evaluation”, “2004-2009 Patent Analysis Report” and “2010 ESI Papers”. Thirty-three public and private universities were selected as the target groups to examine their efficiency. Data Envelopment Analysis (DEA) was used to analyze their efficiency of this framework. The result reveals the public universities’ relatively efficient units are accounted for 34%, while the private universities up to 36% in CCR (Charnes, Cooper & Rhodes model) constant returns to scale. The public universities’ relative efficiency units are accounted for 39%, while the private universities’ efficient units are accounted for 45% in BCC (Banker, Charnes & Cooper model) variable returns to scale. The finding shows that the efficiency of private universities is better than that of public universities.